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Monday, November 11, 2019

Mapping the NLRome: Research Teams Turn to SMRT Sequencing to Trace Plant Immunity

There’s the genome, the transcriptome, the microbiome… and now the NLRome?  Breeders and pathologists have long been interested in uncovering the secrets of plant immunity, and much of their attention has been focused on receptors that can activate immune signalling: cell-surface proteins that recognize microbe-associated molecular patterns (MAMPs), and intracellular proteins that detect pathogen effectors, including nucleotide-binding leucine-rich repeat receptors (NLRs).  Hundreds of NLR genes can be found in the genomes of flowering plants. They are believed to form inflammasome-like structures, or resistosomes, that control cell death following pathogen recognition, and are being investigated as candidates for engineering new pathogen…

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Tuesday, November 5, 2019

Finding the Females: New Reference Genome Leads to Better Sex Determination Technique in Tuna

A team of Japanese researchers has used a new Pacific bluefin tuna reference genome to identify male-specific DNA markers in the fish The cultivation and conservation of one of the most important commercial fishes in the world may come down to sex determination — how can you successfully breed a species without knowing the sex of your stock? A Japanese research team has come up with a solution, thanks to a new Pacific bluefin tuna reference genome and the male-specific DNA markers they were able to identify as a result. In a study published recently in the Nature journal Scientific…

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Friday, September 20, 2019

Sequencing at the Extremes: Low DNA Input Workflow Enables Study of Tiny Ice Worm with Giant Genome

It was the coolest critter Erin Bernberg (@ErinBernberg) had ever worked with – quite literally.  The senior scientist at the University of Delaware Sequencing and Genotyping Center, a PacBio certified service provider, received a shipment of tiny, live ice worms from Washington State University and immediately faced several challenges. How would she get them out of their ice cubes? How would she isolate DNA from the delicate, dark pigmented creatures? And would she be able to extract enough DNA to sequence?  Thanks to the new PacBio low DNA input protocol, the answer to the last question was yes. In fact,…

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Wednesday, June 26, 2019

Application Updates: Introducing Iso-Seq Express for Faster RNA Sequencing

Seeking to sequence and characterize entire transcriptomes in one go? Our new Iso-Seq protocol and reverse-transcriptase PCR kit makes it easier, speedier and cheaper.  Run on the new Sequel II System, the completely revamped Iso-Seq Express workflow achieves whole transcriptome characterization from a single SMRT Cell 8M delivering up to 400 Gb, and at a third of the cost, or less. Yield has also increased on the Sequel System, with 3.0 sequencing chemistry typically delivering up to 30 Gb per SMRT Cell 1M for our RNA sequencing application.  The new protocol requires three times less RNA input (300 ng) and…

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Thursday, June 13, 2019

The SMRT Special: Journal Focuses on Advances in SMRT Sequencing

Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…

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Monday, June 10, 2019

Catching up with Carola and the ‘Solar-Powered’ Sea Slug

Two years ago, Carola Greve and colleagues at the Zoological Research Museum Alexander Koenig in Bonn, Germany, were seeking to #SeqtheSlug as part of the 2017 Plant and Animal SMRT Grant competition, and the popular project was a close runner-up. Greve didn’t give up on her quest to sequence the ‘solar-powered’ sea slug. We caught up with her recently at the SMRT Leiden Scientific Symposium, where her update on the sea slug project earned her a Best Poster award.    Why the sea slug?   Although Mollusca represents the second largest animal phylum with around 85,000 extant species, only 23 mollusc genomes…

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Thursday, May 30, 2019

Unraveling Malaria Mysteries with Long-Read Sequencing

Plasmodium falciparum Malaria is a complicated killer, and efforts to develop effective vaccines have been hindered by gaps in our understanding of both the parasite that causes the infection, Plasmodium falciparum, and its transmitter, the mosquito. Like many virulent parasites, P. falciparum has evaded close genetic scrutiny due to its complex and changing composition. Its 23 Mb haploid genome is extremely AT rich (~80%) and contains stretches of highly repetitive sequences, especially in telomeric and subtelomeric regions. To make matters more complicated, it expands its genetic diversity during mitosis via homologous recombination, leading to the acquisition of new variants of…

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Wednesday, May 15, 2019

SMRT Leiden Symposium Showcases Successes in Clinical and Conservation Genomics

What can a cute, cuddly, stingless bee from the Brazilian rainforest teach us about eusociality and mitochondrial evolution? Natalia S Araujo wants to find out, and she’s not the only one. As the only bee species in which true polygyny (multiple fertile queens in the same colony) occurs, there is great interest in Melipona bicolor, and its mitochondrial genome (mt genome) was one of the first sequenced in bees. But the sequence was incomplete and lacked information about its mitochondrial gene expression pattern. So Araujo, a postdoctoral researcher of animal genomics in the GIGA Institute of the University of Liège,…

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Monday, May 6, 2019

New Sequel II System Enables Rapid Characterization of Invasive Pests

USDA campaign poster to stop the spread of the invasive pest Stop, Scrape, Squash… and Sequence! The latest invasive insect to hit headlines, the spotted lanternfly, has a voracious, indiscriminate appetite, with a particular taste for apples, grapes and maple — bad news for the wine, orchard and syrup industries of New England, where the Asian pest has been spotted. But there’s good news too, thanks to the expanded capacity of the new Sequel II System. USDA scientists were able to generate a high-quality, 2.3 Gb de novo assembly of a field-caught female Lycorma delicatula on a single SMRT Cell…

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Wednesday, May 1, 2019

The Sequencing of the Octoploid Strawberry Genome Uncovers its Evolution

Ángel Vergara Cruces By Ángel Vergara Cruces, Universidad de Málaga Plant geneticists have achieved a sweet feat: the first assembly of the octoploid strawberry genome. As reported in Nature Genetics earlier this year, a team led by Steven J. Knapp of the University of California-Davis and Patrick P. Edger of Michigan State University, identified more than 100,000 genes in their high-quality assembly and annotation of the commercial strawberry, Fragaria x ananassa. The main challenge when assembling a polyploid genome is that similar regions in different subgenomes (so-called homeologous regions) can lead to uncertainty about where to assign a given read…

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Wednesday, April 24, 2019

Now Available: Sequel II System Delivers ~8 Times as Much Data as Previous System

We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…

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Saturday, April 20, 2019

Smoking out Structural Variants in the Cannabis Genome

With its unique medicinal and psychoactive compounds, the popularity of cannabis is spreading… well, like a weed. Now legal in 10 states for recreational use, and in 33 for medical use (with the FDA approval of the first oral cannabis drug for epilepsy on June 25, 2018), the once-forbidden plant is primed to become one of the most talked-about — and valuable — agriculture crops. But what needs to be done to take this promising crop into the clinic? Sound science, accurate testing protocols, and strident tracking systems — all of which can be achieved through genomics, according to Kevin…

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Wednesday, April 17, 2019

German Shepherd Genome Project Fetches Popular Vote

Maya and her partner, Sgt. Nic Banuelos, of the UWPD K9 unit First there was Shadow, the poodle owned by gene-entrepreneur Craig Venter. Then there was Tasha, a female Boxer. Will the next de-coded dog be Maya, a German Shepherd Dog that helps police the campus at the University of Wisconsin-Madison? Maya has been basking in social media celebrity alongside her human companion Sgt. Nic Banuelos, PhD students Lauren Baker and Emily Binversie, technician Jorden Gruel, veterinary surgeon-scientists Susannah Sample and Peter Muir, and Peter’s woven likeness, after winning the 2019 Plant and Animal SMRT Grant, co-sponsored by Histogenetics. We…

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Tuesday, March 26, 2019

New Isoform-Level Transcriptome Reference Helps Shrimp Industry Ward Off Disease

One of the fastest growing global foods is also one of its most vulnerable. Without an adaptive immune system, the Pacific white shrimp, Litopenaeus vannamei, rely on cellular and humoral defenses, such as the release of antimicrobial peptides, in their battle against invading microbes and pathogen infections. A battle they’re losing, leading to massive mortality and devastating economic losses. A full-length transcriptome analysis using the PacBio Iso-Seq method has resulted in an isoform-level reference transcriptome that is shedding new light into the shrimp’s innate immune system, providing hope for the shrimp aquaculture industry. One of the most economically important shrimp…

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Thursday, March 21, 2019

Two New Reference Genomes Expand Potential for Millet as Super Cereal Crop

The modern world might benefit from a return to our ancient roots by expanding the cultivation of one of the first domesticated crops, broomcorn millet. Foodies will appreciate that the crop, a staple in many semi-arid regions of Asia and Europe, is gluten-free and extremely nutritious, with higher levels of protein, several minerals, and antioxidants than most other cereals. Farmers will appreciate that the drought-resistant plant has the highest water-use efficiency among all cereal crops, (i.e. the highest amount of grains produced with the same amount of water), a short life cycle (60–90 days), and a high harvest index. And…

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